StartStructClaimer.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file TopologyBroker
/// @brief  top-class (Organizer) of the TopologyBroker mechanism
/// @detailed responsibilities:
/// @author Oliver Lange

// Unit Headers
#include <protocols/topology_broker/StartStructClaimer.hh>

// Package Headers
#include <protocols/topology_broker/DofClaim.hh>
#include <protocols/topology_broker/Exceptions.hh>
// Project Headers
#include <core/pose/Pose.hh>

#include <core/chemical/ChemicalManager.hh>
// AUTO-REMOVED
// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>

#include <core/fragment/FragSet.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/util.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/BBTorsionSRFD.hh>

#include <protocols/simple_moves/FragmentMover.hh>

// ObjexxFCL Headers

// Utility headers
#include <utility/excn/Exceptions.hh>
//#include <utility/io/izstream.hh>
//#include <utility/io/ozstream.hh>
//#include <utility/io/util.hh>
#include <basic/Tracer.hh>
//#include <basic/options/option.hh>
#include <numeric/random/random.hh>

#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>


//// C++ headers

static numeric::random::RandomGenerator RG(199234234);


static basic::Tracer tr("protocols.topo_broker",basic::t_info);
//static numeric::random::RandomGenerator RG(181134);

namespace protocols {
namespace topology_broker {

using namespace core;

StartStructClaimer::StartStructClaimer() : bUseInputPose_( true ), perturb_( 0.0 )
{
  set_claim_right( DofClaim::INIT );
  set_bInitDofs( true );
}

StartStructClaimer::StartStructClaimer( core::pose::Pose const& pose ) : bUseInputPose_( true ), perturb_( 0.0 )
{
  set_claim_right( DofClaim::INIT );
  //  generate_init_frags( pose );
  start_pose_ = pose;
  set_bInitDofs( true );
}

void StartStructClaimer::new_decoy() {
  //  start_pose_.clear();
}

void StartStructClaimer::new_decoy( core::pose::Pose const& pose ) {
  if ( bUseInputPose_ ) {
    start_pose_ = pose;
  }
  //CANNOT do this here since SEQUENCE_CLAIMS need to be resolved first to know the sequence-offset
  // generate_init_frags( start_pose_ );

  //  start_pose_.clear();
}

void StartStructClaimer::generate_sequence_claims( DofClaims& new_claims ) {
  new_claims.push_back( new SequenceClaim( this, 0, 0, label(), DofClaim::NEED_TO_KNOW /* for now... eventually CAN_INIT ? */ ) );
}

void StartStructClaimer::generate_init_frags( core::pose::Pose const& pose ) {
  std::set< Size > start_region;
  get_sequence_region( start_region );
  //for ( Size i = 1; i<= pose.total_residue(); ++i ) {
  //    start_region.insert( i );
  //  }
  if (tr.Trace.visible() ) {
    tr.Trace << " start region for StartStructClaimer "<< std::endl;
    for ( std::set< Size >::iterator it = start_region.begin(); it != start_region.end(); ++it ) {
      tr.Trace << *it << " ";
    }
    tr.Trace << std::endl;
  }


  using namespace fragment;
  ConstantLengthFragSetOP fragset = new ConstantLengthFragSet( 1 );
  steal_frag_set_from_pose( pose, *fragset, new FragData( new BBTorsionSRFD, 1 ), start_region );
  simple_moves::ClassicFragmentMoverOP mover = new simple_moves::ClassicFragmentMover( fragset );
  mover->set_check_ss( false ); /* not good if we want to initialize from 1mer fragments */
  set_mover( mover );

}

void StartStructClaimer::initialize_residues( core::pose::Pose&, SequenceClaimOP , DofClaims&  ) {
  //now the sequence is known:
  if ( start_pose_.total_residue() > 0 ) {
    generate_init_frags( start_pose_ ); //requires sequence definition --- had to wait until now.
  }
  //start_pose_.clear(); // save the space..
}


void StartStructClaimer::initialize_dofs(
     core::pose::Pose& pose,
     DofClaims const& init_dofs,
     DofClaims& failed_to_init
) {

  try{
    mover();
  } catch( utility::excn::EXCN_NullPointer excn ) {
    throw( EXCN_Input( "StartStructureClaimer needs JobInputter or FILE <pdb-file> entry in broker-setup"));
  }

  FragmentClaimer::initialize_dofs( pose, init_dofs, failed_to_init );
  if ( perturb_ == 0.0 ) return;
  for ( DofClaims::const_iterator it = init_dofs.begin(), eit = init_dofs.end();
        it != eit; ++it ) {
    //don't really know how this looks for jumps
    if ( (*it)->type() == DofClaim::BB ) {
      Size pos( (*it)->pos( 1 ) );
      pose.set_phi( pos, pose.phi( pos ) + RG.gaussian()*perturb_ );
      pose.set_psi( pos, pose.psi( pos ) + RG.gaussian()*perturb_ );
    }
  }
}

bool StartStructClaimer::read_tag( std::string tag, std::istream& is ) {
  if ( tag == "file" || tag == "FILE" ) {
    std::string filename;
    is >> filename;
    tr.Debug << type() << " initialized with file " << filename << std::endl;
    core::pose::Pose pose;
    core::import_pose::pose_from_pdb( start_pose_,
      *core::chemical::ChemicalManager::get_instance()->residue_type_set( core::chemical::CENTROID ),
      filename );
  } else if ( tag == "PERTURB" ) {
    is >> perturb_;
  } else if ( tag =="NO_USE_INPUT_POSE" ) {
    bUseInputPose_ = false;
  } else return FragmentClaimer::read_tag( tag, is );
  return true;
}



} //topology_broker
} //protocols